350 rancher front cover install

I just did my first case split on my 01 rancher to change cranks. MY local shop wanted $650 with me taking them the motor and the crank, so I figured WTH I’ll try it. When I started installing the front cover the crank (used) is not going into the bearing in the cover as easily as I would like it to. So before I break something while figuring it out, any tips? Also is ultra grey permatex ok to seal the cases or do I need to get honda bond and start again?
Thanks in advance.